Special Topics: Evolutionary Trees (BIOL410)
This course is an Introduction to Phylogenetics, the biological discipline responsible of disentangling the evolutionary history and relationships among all living organisms. Since “Nothing in biology makes sense except in the light of evolution”, we will be spending the next weeks making sense out of biology by learning how to see organisms in evolutionary perspective and turn phenomena into stories.
In particular, after taking this course you will be able to: 1) Understand and discuss how evolutionary history is reconstructed and why it matters; 2) Create your own phylogenetic trees using molecular data freely available and applying different bioinformatic methods; and 3) Improve your skills reading and discussing critically current scientific literature.
These three objectives are connected to all the campus-wide learning outcomes of related to Intellectual Sophistication: Understand, Analyze, and Interpret. They are also reflected in the IDEA objectives of gaining a basic understanding of a subject; developing specific skills needed by professionals in the field; and learning appropriate methods for collecting, analyzing, and interpreting information.
General Botany (BIOL 220). 2016-2017 (Fall and winter terms). 2017-2018 (Winter)
This course is an introduction to botany, the scientific study of plants. The focus is mainly on flowering plants, although the rest of the lineages of the “green line” are also covered. The main goal is to help the student understand the biological aspects of these organisms (morphology, physiology, systematics, evolution and ecology) and their essential role in worldwide ecology, human society and economics. In other words: we will work to overcome the so-called plant blindness, defined as “…the inability to see or notice the plants in one’s own environment—leading to: (a) the inability to recognize the importance of plants in the biosphere, and in human affairs; (b) the inability to appreciate the aesthetic and unique biological features of the life forms belonging to the Plant Kingdom; and (c) the misguided, anthropocentric ranking of plants as inferior to animals, leading to the erroneous conclusion that they are unworthy of human consideration.” (Wandersee & Schussler 1998).
Teaching resources for General Botany
I am developing an in-class activity to simulate the process of the description of a new species in a gamification environment. The activity is still under development and I will upload the resources here once it is ready, but you are free to contact me if you want to know more. I presented it at the XIX IBC (Shenzhen, 2017) during the symposium T06-4 (Prescriptions for overcoming plant blindness).
Title: Biodiversity Description Simulation: a Tool to Stimulate Interest in Plant Taxonomy during Class
Abstract: Many future biologists complete their college education with just minimal training on plant biology, and the lack of time and resources make impossible a deeper immersion in plant taxonomy practice and the description of biodiversity during an introductory course. If the students are never exposed to this field, it becomes harder for them to gain the appreciation or pursue their interest on a field that would be so needful in the next generation of biologists. The activity proposed here is designed to stimulate the interest on taxonomy with a game in which groups of students simulate to compete to be the first to describe and publish a new plant species. This activity has been tested successfully with classes of about 40 students in a time frame of 75 minutes, which make it suitable to fit in a single class or lab session. The students are divided in a variable number of groups with three different roles: explorers, editors and curators. Each group receives a different briefing depending on their role: to identify a plant and send a manuscript with its description; to review submitted manuscripts and publish them when they comply with the code of nomenclature; and to accession and database plant specimens in a herbarium. The skills needed to participate in the game can be adjusted to the desired competencies of an introductory botany course. The debriefing discussion may include topics such as the challenges of biodiversity description, the peer-reviewed publication process and the importance of scientific collections.
Directed Study: Botanical Illustration (BIOL499)
Course Goals: This hands-on course has as its main objective to develop and practice skills and techniques of scientific botanical illustration based both on fresh material and herbarium specimens. The enrolled students will receive a guided and personalized series of assessments to illustrate plants and reflect on the purpose of this activity. The students will also improve their understanding on plant anatomy and taxonomy. These goals are aligned with the college-wide learning outcomes of Disciplinary Knowledge and Creative Thinking.
The instructor and the students will meet regularly on Fridays to review the progress, discuss the new material and establish the assignment for the following week. The students are supposed to work independently on Monday and Wednesday, although they are encouraged to communicate with the instructor when they consider it relevant.
Prerequisites: BIOL220 (General Botany)
Fundamentals of Ecology (BIOL180). 2016-2017; 2017-2018. (Spring)
This course is an introduction to ecology, the scientific discipline that studies the interconnections of living organisms with their environment and among them. During the first weeks we will explore these relationships at different scales from a descriptive point of view. The second part of the course will be devoted to the study of the relationship of the human species with its environment from an ecological perspective, with special emphasis on sustainability as a core concept. This is a PN course (Perspectives on the Natural World) as defined by the General Education Committee of the college.
Biological Principles (BIOL101). 2017-2018 (Fall)
This course is an invitation to Biology, the vast scientific discipline that encompasses the study of life in all its forms and at all its levels. Obviously, it will be impossible to cover this entire subject within only 10 weeks, but we will approach a number of fundamental topics that deserve attention from a broad perspective. This course will be structured in three blocks aligned with three different levels of organization of the phenomenon of life: molecules and cells; organisms and evolution; ecology and biogeography.
Our ultimate goal will be to discuss the origin and legitimacy of the scientific knowledge in our society and how to identify and debunk pseudoscience. In a nutshell, we will be improving our scientific literacy as defined by Neil deGrasse Tyson:
UCONN EEB3899-007: A primer for practical phylogenetic data gathering
During the Spring semester of 2015, Dr. Yang Liu and I designed and implemented a one-credit seminar specifically targeted for undergraduate students that were starting their experience in research labs as trainees in DNA extraction, amplification and analysis. It is fairly common to see students at the EEB department getting involved in this kind of research, but although they can become competent at the lab tasks, there is usually limited time for them to understand the “big picture” or to receive a proper training in phylogenetic analysis (since these specific skills requires more advanced background and an extensive dedication to be mastered). At the same time, there are many minor skills or activities that they can acquire during their time in the lab (preparation of files for submission to GenBank, primer design, troubleshooting, basic edition of alignments, etc) that we thought should be incorporated into their learning experience.
We designed the seminar with the following specific objectives, covering first the practical issues that they need to understand for their activity in the lab from the very beginning:
- Background for lab and computer activities: a) Understanding the rationale of the work in a lab (DNA extraction, PCR and Sanger sequencing) as well as providing the tools to develop their own troubleshooting tests; b) A Genbank primer for BLAST, sequence retrieval and preparation of sequence submission and c) Background and basic tools of sequence alignment
- A very brief theoretical introduction to phylogenetic analysis and evolutionary trees
- Discussion of scientific papers or essays dealing with the topics addressed in other sessions
- Generation of distance-based phylogenetic trees
The seminar was structured in 12 sessions of 50 minutes plus a final invited talk:
EEB3899-007_session 1. DNA extraction, amplification and sequencing
EEB3899-007_session 2. Troubleshooting. Nested PCR. Primer design
EEB3899-007_session 3. Sequence manipulation. Retrieving sequences from GenBank
EEB3899-007_session 4. Sequence formats. Alignments
EEB3899-007_session 5. Uploading sequences to GenBank
EEB3899-007 session 6: discussion of the essay “Integrating DNA barcode data and taxonomic practice: Determination, discovery and description” (Goldstein & DeSalle, 2010. Bioessays 33: 135-147)
EEB3899-007_sessions 7 &_8. Evolution, phylogeny and classification. Cladistics. Properties and uses of phylogenetic trees
EEB3899-007 session 9: discussion of the paper “Convergent sequence evolution between echolocating bats and dolphins” (Liu et al., 2015. Current Biology 20: R54)
EEB3899-007_session 10. Using molecules as data. Types of homology. Primary and secondary structure. The ITS region
Session 11: discussion of the paper “Testing reticulation and adaptive convergence in the Grimmiaceae (Bryophyta)” (Henández-Maqueda, Quandt & Muñoz. 2008. Taxon 57: 500-510)
EEB3899-007_session12. Generation of distance-based phylogenetic trees
Final session: Emily Behling, an undergraduate student in the Goffinet lab, shared her research experience
Teaching assistance at Universidad Autónoma de Madrid
Botany (for Biology majors). 2003-2012 (7 courses). Laboratory and field
Botany (for Environmental Science majors). 2003-2004; 2009-2011 (3 courses). Laboratory and other activities
Introduction to the Iberian Flora. 2005-2007 (2 courses). Laboratory and field; 2005-2006 (1 course). Laboratory
Cryptogamy. 2005-2006. (1 course) Laboratory
Advanced laboratory; Terrestrial ecosystems. 2008-2009 (1 course). Field